How can we reference a shipment for payment, instead of individual lines of different POs?

We receive material from overseas.  Our vendors almost always combine numerous POs (some partial) in one shipment.  This causes our AP department to have to search for lines in numerous POs and is very time consuming.

Will receipt routing allow us to be able to easily pay for what shipped regardless of what PO the material belongs to?  For example by referencing a shipment, as opposed to lines of individual POs.  I was cautioned against using inbound transportation by a consultant.

Is inbound transportation the only option?